tbuckley/cabot-search huggingface dataset:
Abstract 651: Revealing the role of lung cancer microbiota in the tumor progression
Authors: Erick M. Riquelme, Ivania Valdes, Carlos Aravena, Ilse Valencia, Barbara Mino, Daniel Carvajal, Alberto Martin
Journal: Cancer Research (2023)

Abstract Lung cancer (LC) remains as the leading cause of death by cancer worldwide. In Chile, LC is the second cause of cancer-related deaths. Recently, studies in melanoma and non-small cell lung cancer (NSCLC) patients have highlighted the role of the gut microbiota as an important host factor in mediating the responses/resistance to immunotherapy, suggesting that bacteria present in the gut may modulate the immune response in these tumors. However, the role of extra-intestinal microbiota; bacteria living outside of the gut, in cancer pathogenesis and the response to anti-cancer therapies remains largely undetermined. Here we characterize the composition of intratumoral microbiota of NSCLC and seek to establish a functional relationship between it and the composition of the immune microenvironment and the clinicopathological characteristics of NSCLC patients. From the first 157 FFPE NSCLC samples, we extracted DNA from all collected samples, obtaining adequate material in quality and quantity to later be submitted for analysis to 16S sequencing. Using 16S rRNA gene sequencing, we assessed the general landscape of the NSCLC tumor microbiome, revealing the presence of large number of bacterial communities in the NSCLC tumor samples on the different histological subtypes analyzed. We have detected differences in alpha diversity in the histological subtypes studied. Even more interesting, we have detected significant differences in lung adenocarcinoma depending on the degree of histological differentiation, observing a decrease in proteobacteria and an enrichment of Bacteroidales, as cell differentiation is lost. Additionally, we identified taxonomic differences between differentiated and undifferentiated tumors. Differentiated tumors show enrichment in Akkermansia muciniphila and while undifferentiated tumors show enrichment in Actinobacter Corynebacterium. Suggesting that these taxa could contribute to maintaining a differentiated state or inducing cell dedifferentiation, respectively. Our results reveal the presence of a large number of bacterial communities in lung cancer samples in the different histological subtypes analyzed. Suggesting that these communities could play a key role in tumor differentiation and progression. Citation Format: Erick M. Riquelme, Ivania Valdes, Carlos Aravena, Ilse Valencia, Barbara Mino, Daniel Carvajal, Alberto Martin. Revealing the role of lung cancer microbiota in the tumor progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 651.
Abstract 3602: The metastasis-suppressive function of intracellular galectin-3 in melanoma
Authors: Norhan B. B. Mohammed, Charles J. Dimitroff
Journal: Cancer Research (2023)

Abstract Melanoma is a relatively rare skin cancer. However, it accounts for most of all skin cancer-related deaths worldwide. Once melanoma spreads to distant sites, it confers a poor prognosis characterized by resistance to therapy and high mortality rate. Hence, a favorable clinical outcome is strongly correlated with early diagnosis. Despite the ongoing research to identify novel diagnostic, prognostic, and therapeutic targets for metastatic melanoma (MM), a reliable serum marker to predict whether melanoma is vulnerable to metastasize or has already metastasized is still lacking. Galectin-3 (Gal-3), a ß-galactoside-binding protein, is widely expressed by many human epithelial and immune cells. High extracellular Gal-3 expression levels have been reported to be positively correlated with late-stage disease in melanoma patients, where it is theorized to bind surface glycosylated proteins to promote melanoma cell invasion and metastasis. Gal-3 is also expressed intracellularly where it participates in the regulation of many biological processes. However, intrinsic Gal-3 levels within the melanoma cell and its relationship to melanoma progression is still poorly understood. Using The Cancer Genome Atlas (TCGA) database, we analyzed the Gal-3 expression profiles of 471 tumor samples obtained from melanoma patients. To our surprise, TCGA data analysis has shown significantly higher expression of Gal-3 in primary melanoma samples compared to metastatic melanoma. We hypothesize that intracellular Gal-3 potentially negatively regulates primary melanoma progression to metastatic disease. Using several human melanoma cell lines silenced for Gal-3 expression, we investigated the corresponding malignancy-associated activities of these cells. Our results revealed that Gal-3 silencing in melanoma cells potentiated melanoma migration, invasion, and colony formation, compared with mock controls, suggesting that intracellular Gal-3 could interfere with melanoma metastatic activity. Moreover, loss of Gal-3 boosted the activation of the PI3K/AKT and MAPK signaling pathways and upregulated nuclear factor of activated T cells (NFAT1) expression and its pro-metastatic downstream target genes. Importantly, this study illuminates the apparent opposing roles of Gal-3 in melanoma progression, with intracellular Gal-3 potentially serving as a metastasis-suppressive molecule. Moreover, these studies reveal the potential of analyzing melanoma cell-intrinsic levels of Gal-3 to better predict metastatic potential and clinical outcome in melanoma patients. Citation Format: Norhan B. B. Mohammed, Charles J. Dimitroff. The metastasis-suppressive function of intracellular galectin-3 in melanoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3602.
Abstract 4464: Comparison of two DTH models for T cell-mediated immunity in preclinical screen
Authors: Yingying Cai
Journal: Cancer Research (2023)

Abstract Introduction: Delayed-type hypersensitivity (DTH) involves the recruitment of T cells into tissues and the activation by antigen-presenting cells to produce cytokines, which further activates local endothelial cells and recruits macrophages, resulting in tissue erythema, swelling and inflammation. DTH models in mice are classical in-vivo T cell-mediated immunity screening models for atopic dermatitis, asthma and autoimmune diseases. Different antigens and haptens have been used to establish DTH models with different Th1/Th2 profiles. More immunity characterization of the most widely used DTH models need to be revealed. Results: We established DNFB, Oxazolone induced DTH models in both BALB/c and C57BL/6 mice with ear thickness as the readout. At the termination, we measured Th1 (ie, IFN-γ)/Th2 (ie, IL-4) profile, pro-inflammatory cytokines including IL-13, TNF, and IL-17 as well as myeloperoxidase (MPO) activity from mice ears as indices to score the degree of inflammation. Oxazolone in BALB/c exhibited more repeatable and robust window in Th1/Th2 balance and cytokines profiles. The comparison of two DTH models were further validated by the pathological analysis for cell infiltration in mouse ears and immune-phenotyping in spleen by FACS. Conclusion: The comparison of DNFB and Oxazolone induced DTH models characterized the disease progression and established a more comprehensive preclinical DTH model with well-defined Th1/Th2 profile for the drug efficacy evaluation in the T cell-mediated immune response. Key words: Delayed-type hypersensitivity, mice model, T cell-mediated Citation Format: Yingying Cai. Comparison of two DTH models for T cell-mediated immunity in preclinical screen. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4464.
Abstract 497: HX301, a first-in-class ARK5i, demonstrates antitumor activity in preclinical HCC models with high ARK5/Myc expression
Authors: Zhihua Jiao, Jingjing Wang, Hang Ke, Faming Zhang, Henry Li
Journal: Cancer Research (2023)

Abstract Introduction: Hepatocellular carcinoma (HCC) is an aggressive malignance of high mortality (6th most common worldwide) with few treatment options. Current drug treatments, including chemo-/target therapies (e.g., sorafenib), are usually ineffective among advanced HCC and with high toxicity. ARK5, or NUAK1, a novel AMP-activated protein kinase (AMPK) family member 5, is found overexpressed in many malignancies including HCC and usually associated with poor prognosis, as well as drug resistance. For example, doxorubicin, first-line chemotherapy for TACE, and transarterial chemoembolization for advanced HCC. In addition, ARK5 is found to be vitally involved in oncoprotein Myc-driven oncogenesis (metabolic homeostasis/cell survival), particularly in tumors under nutrition/oxygen-deprivations, including HCC. HX301 is a clinical stage first-in-class (FIC) ARK5 inhibitor (ARK5i) and other kinase activities (e.g., CDK4/6, CSF1R, etc.). In this study we evaluate HX301 antitumor activity in HCC over-expressing both ARK5 and c-Myc. Methods: A panel of subcutaneous HCC patient-derived xenografts (PDXs) were genomically profiled by whole transcriptome sequencing by RNAseq, and several selected models with different expression of ARK5 and c-myc expression were assessed pharmacologically using daily dosing of 100mg/kg HX301. Subcutaneous tumor responses to HX301 were calculated by tumor growth inhibition (TGI). Results: HCC PDX models LI1035, LI6610 both had high expression of ARK5 and Myc genes, whereas LI6650 had lower expression level of Myc than LI1035 and LI6610. LI6652 had lower expression level of ARK5 than LI1035 and LI6610. The log2 FPKM values of ARK5 and Myc in model of LI1035 was 3.9284 and 4.8177, 3.6629 and 5.3658 for LI6610, 3.1228 and -0.0556 for LI6650, -0.3538 and 6.5785 for LI6652. The TGI for LI1035 and LI6610 was 64% (P = 0.0293) and 62% (P = 0.0257) respectively whereas in comparison a smaller TGI of 44% (P = 0.034) was observed in LI6650. In the model of LI6652, TGI for HX301 was 58%, but a statistically significant difference was not observed when comparing the treatment group with the vehicle group (P = 0.138). Conclusions: Our preliminary results demonstrate that HX301 had strong antitumor activity in HCC PDX models expressing both ARK5 and c-Myc. HX301 has the potential to be a first-in-class ARK5i candidate for the treatment of advanced HCC with high expression of c-Myc, warranting further clinical investigation. Citation Format: Zhihua Jiao, Jingjing Wang, Hang Ke, Faming Zhang, Henry Li. HX301, a first-in-class ARK5i, demonstrates antitumor activity in preclinical HCC models with high ARK5/Myc expression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 497.
Abstract 764: Automated walk away NGS sample preparation for constructing in-line molecular barcoded RNA libraries from Fresh Frozen and FFPE samples
Authors: Saharnaz Bigdeli, Bahram Arezi, Jan Godoski, Denise Rhodes, Ryan Aguilar, Karen William, Bernd Buehler, Ji Zhu, Ronda Allen
Journal: Cancer Research (2023)

Abstract RNA-Seq is a revolutionary technology for transcriptome analysis, which has been used to quantify transcript levels, confirm gene annotation, identify novel transcripts, splice variants, and fusion detection. Traditionally, the usefulness of RNA-Seq has been limited by pre-analytical (sample availability, low integrity, tumor heterogeneity, complex protocols) and analytical factors (small mRNA fraction, high read duplicate rate), which can lead to higher costs, longer turnaround times, and false negative results. We have developed and automated a streamlined workflow for construction of highly complex RNA Libraries from fresh frozen and FFPE samples that addresses these concerns. We use target enrichment by bait selection with FFPE-derived samples, where rRNA depletion is found to be inconsistent and poly(A) enrichment cannot be used due to degradation of the source material. A fully automated protocol using pre-aliquoted reagents, has been optimized on the Magnis NGS Prep System for a wide range of RNA inputs (10-200 ng), various sample types (Intact and FFPE total RNA) and equipped with 192 Unique Dual sample Indices (UDI) to minimize the effects of possible index hopping and contamination. Addition of in-line molecular barcodes incorporated at the ligation step helps differentiate fragmentation from PCR duplicates, which increases the total number of reads available for further analysis (gene expression and fusion detection). With minimal risk of contamination, this automated protocol delivers up to eight target-enriched NGS Illumina sequencing-ready cDNA libraries from total RNA input per run in about 12 hours without the need of any user intervention. Both catalog and custom probes can be utilized, and PCR cycles can easily be adjusted from the touchscreen to optimize the library yields. For Research Use Only. Not for use in Diagnostic procedures. Citation Format: Saharnaz Bigdeli, Bahram Arezi, Jan Godoski, Denise Rhodes, Ryan Aguilar, Karen William, Bernd Buehler, Ji Zhu, Ronda Allen. Automated walk away NGS sample preparation for constructing in-line molecular barcoded RNA libraries from Fresh Frozen and FFPE samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 764.
Abstract 3569: An animal model of GLI2-amplified medulloblastoma
Authors: Yanxin Pei
Journal: Cancer Research (2023)

Abstract Medulloblastoma (MB) is the most common malignant brain tumor affecting children. Among the known subtypes of MB, GLI2-amplified SHH-MB associated with P53 mutations has the worst prognosis, and a 5-year survival rate of less than 30%. Moreover, GLI2-amplified MBs are non-responsive to SMO inhibitors, the only targeted treatment option available for SHH-MB. To address this treatment gap, there is an urgent need to identify novel potential therapeutic targets, an effort that requires better understanding of key cellular and molecular mechanisms underlying GLI2-amplified MB. To that end, we generated a mouse model of GLI2-amplified MB and identified GL12 as the critical driver of tumorigenesis, and granule cell progenitors (GCPs) as the cells of tumor origin. We further found that GLI2 specifically drives embryonic, but not neonatal, Math1+ GCPs to form SHH-MB tumors. An scRNA-seq analysis revealed MAPK pathway activation specifically in embryonic Math1+ GCPs. The MAPK pathway was activated in mouse and human GLI2-driven MB tumors, and a MEK/ERK inhibitor significantly inhibited GLI2-driven MB in vivo. Based on these findings, we hypothesize that GLI2-driven MB originates from a specific population of Math1+ GCPs during a discrete temporal interval in cerebellar development, and that targeting MAPK/MEK/ERK pathway components represents a novel approach to treatment of GLI2-amplified MB. Citation Format: Yanxin Pei. An animal model of GLI2-amplified medulloblastoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3569.
Abstract 4466: Inhibition of ERO1a and IDO1 improves dendritic cell infiltration into pancreatic ductal adenocarcinoma
Authors: Apple Tay, Andreas Lundqvist, Siu Kwan Sze
Journal: Cancer Research (2023)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is one of the most hypoxic, lethal, and treatment resistant cancers. Due to its desmoplasias along with the hypoxic state and scarce infiltration of T cells, PDAC is considered a cold tumor. Using a proteomic approach, we previously identified that the expression of endoplasmic reticulum oxidoreductase 1 alpha (ERO1α) is induced by hypoxia and correlates with reduced survival in PDAC. Furthermore, we observed an increased kynurenine formation under hypoxia, suggesting a role of indoleamine 2,3-dioxygenases (IDO1) in PDAC. Since ERO1α and IDO are involved in driving immune suppression through influencing the generation of immature myeloid cells, we sought to investigate whether inhibition of these pathways modulates the myeloid cell composition in PDAC. Using MiaPaCa2 as a PDAC spheroid model with hypoxic core grown in serum-free defined media and immune cell infiltration, we assessed the functional role of ERO1a with IDO1 in modulating monocyte infiltration and differentiation into pro- and anti-inflammatory phenotypes, followed by characterizing the immunomodulatory factors secreted using tandem mass spectrometry. Inhibition of ERO1a and IDO1 significantly improved U937 monocyte infiltration (p-value = ****) and differentiation into dendritic cells (p-value = ****). Secretome analysis of proteins identified with high false discovery rate (q-value&amp;lt;0.01) revealed a downregulation of hypoxia and pancreatic cancer pathways in PDAC spheroids. In the presence of monocytes, upregulation of immune-related pathways for antigen presentation (15-fold) and myeloid cell maintenance signaling (2-fold) were observed. Moreover, specific immune-modulatory factors involved in immune infiltration and migration including interleukin 8, lymphocyte cytosolic protein 1 and transgelin-2 were upregulated at 27-, 20-, and 14-fold respectively. Taken together, these results indicate that inhibition of ERO1a and IDO1 drives an inflamed tumor microenvironment associated with improved monocyte infiltration and differentiation into dendritic cells to potentially enable T cell infiltration and killing of PDAC tumors. Citation Format: Apple Tay, Andreas Lundqvist, Siu Kwan Sze. Inhibition of ERO1a and IDO1 improves dendritic cell infiltration into pancreatic ductal adenocarcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4466.
Abstract 4971: Identification of statins as a potential treatment for ovarian cancer 
Authors: Brendan M. Reilly, Sarah J. Miseirvitch, Sarah R. Walker
Journal: Cancer Research (2023)

Abstract Late-stage diagnoses make ovarian cancer extremely hard to treat. This leads to ovarian cancer accounting for 5% of female cancer deaths and 2.5% of female cancer incidence. Since there are few options for early detection of ovarian cancer, targeted therapies could lead to better outcomes. One target that has been implicated in ovarian cancer, is the transcription factor Signal Transducer and Activator of Transcription 3 (STAT3). STAT3 function is associated with tumor growth, metastasis, drug resistance, angiogenesis, and resistance to apoptosis. These many STAT3 controlled, cancer-associated cellular functions, make it an ideal and versatile target for cancer therapy. Using the Broad institute’s online C.L.U.E. tool and a STAT3 gene signature, we identified statin drugs as potential inhibitors of STAT3 activity. To assess the ability of statins to inhibit STAT3, we treated ovarian cancer spheroids with statins and analyzed STAT3 activity. We have found that statins do not induce a change in the phosphorylation of STAT3 on either tyrosine 705 or serine 727 residues, the two major sites of phosphorylation on STAT3. However, there are other poorly understood post-translational modifications of STAT3, that have previously shown effects on STAT3 function, that may be involved. Importantly, we have observed that statin treatment reduces the viability of Ovcar8 and Heya8 ovarian cancer cell spheroids. We also found that statin treatment induced apoptosis of ovarian spheroids by measuring Annexin V staining. A major problem for ovarian cancer patients is metastasis. Our preliminary evidence suggests that statins reduce the ability of ovarian cancer spheroids to clear a mesothelial monolayer of cells, an early step in ovarian cancer metastasis. There are several membrane-associated signaling proteins, including RAF and RAS, that affect STAT3 activity. Both Ovcar8 and Heya8 spheroids showed a decrease in cell viability with statin treatment, which is partially rescued by geranylgeranyl pyrophosphate (GGPP), a downstream metabolite in the mevalonate pathway. The partial recovery by GGPP indicates a mechanism involving the prenylation of membrane associated proteins. This data shows statins may provide effective treatments for ovarian cancer and defining the mechanisms behind the effects of statins may lead to better therapies and outcomes for ovarian cancer patients Citation Format: Brendan M. Reilly, Sarah J. Miseirvitch, Sarah R. Walker. Identification of statins as a potential treatment for ovarian cancer . [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4971.
Abstract 4465: Evaluation of tumor draining lymph nodes in dogs with spontaneously arising osteosarcoma using single-cell sequencing
Authors: Samuel A. Brill, Dylan T. Ammons, Anne C. Avery, Douglas H. Thamm
Journal: Cancer Research (2023)

Abstract Tumor draining lymph nodes (TDLNs) function as an anatomic niche which primes immune cells to generate anti-cancer responses. While tumors are frequently staged based on the presence or absence of TDLN metastasis, mechanisms for how tumors impact the TDLN microenvironment and immunologic responses are incompletely understood. Dogs with spontaneously arising tumors provide an opportune model to study immuno-oncology, sharing many similarities to human patients with their environment, clinical care, and pathobiology. To evaluate how tumors impact TDLN responses, we conducted single cell RNA sequencing (scSeq) on cryopreserved TDLNs of dogs with osteosarcoma (n=4) and healthy controls (n=2). We obtained an average of 3,984 cells per sample (range 1,603-5,259) with a total of 4,780 cells from healthy samples and 19,121 cells from TDLN samples. All samples were integrated into one dataset, then unsupervised clustering was completed. Each unique cell cluster was assigned an identity using canonical markers and reference mapping to human datasets. Following cell classification, we observed notable changes in gene expression across all cells isolated from the LNs, with most differences arising from changes to the transcriptome of myeloid cells. Although still preliminary, the data also demonstrate differences in the abundance of T, B, and myeloid cells between healthy and tumor draining LNs. Taken together, this dataset provides indications of the changes TDLNs undergo in dogs with osteosarcoma. Citation Format: Samuel A. Brill, Dylan T. Ammons, Anne C. Avery, Douglas H. Thamm. Evaluation of tumor draining lymph nodes in dogs with spontaneously arising osteosarcoma using single-cell sequencing. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4465.